WEScover: selection between clinical whole exome sequencing and gene panel testing
Abstract Background Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted ge...
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doaj-1eed6270bc814a5da9868696bb4f71772021-05-23T11:48:50ZengBMCBMC Bioinformatics1471-21052021-05-012211910.1186/s12859-021-04178-5WEScover: selection between clinical whole exome sequencing and gene panel testingIn-Hee Lee0Yufei Lin1William Jefferson Alvarez2Carles Hernandez-Ferrer3Kenneth D. Mandl4Sek Won Kong5Computational Health Informatics Program, Boston Children’s HospitalComputational Health Informatics Program, Boston Children’s HospitalComputational Health Informatics Program, Boston Children’s HospitalComputational Health Informatics Program, Boston Children’s HospitalComputational Health Informatics Program, Boston Children’s HospitalComputational Health Informatics Program, Boston Children’s HospitalAbstract Background Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted gene panel testing may be a dependable option to ascertain true negatives for genomic variants in known disease-associated genes. We developed a web-based tool to quickly gauge whether all genes of interest would be reliably covered by WES or whether targeted gene panel testing should be considered instead to minimize false negatives in candidate genes. Results WEScover is a novel web application that provides an intuitive user interface for discovering breadth and depth of coverage across population-scale WES datasets, searching either by phenotype, by targeted gene panel(s) or by gene(s). Moreover, the application shows metrics from the Genome Aggregation Database to provide gene-centric view on breadth of coverage. Conclusions WEScover allows users to efficiently query genes and phenotypes for the coverage of associated exons by WES and recommends use of panel tests for the genes with potential incomplete coverage by WES.https://doi.org/10.1186/s12859-021-04178-5Genetic testingFalse negativeCoverageWhole exome sequencingGene panel testing |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
In-Hee Lee Yufei Lin William Jefferson Alvarez Carles Hernandez-Ferrer Kenneth D. Mandl Sek Won Kong |
spellingShingle |
In-Hee Lee Yufei Lin William Jefferson Alvarez Carles Hernandez-Ferrer Kenneth D. Mandl Sek Won Kong WEScover: selection between clinical whole exome sequencing and gene panel testing BMC Bioinformatics Genetic testing False negative Coverage Whole exome sequencing Gene panel testing |
author_facet |
In-Hee Lee Yufei Lin William Jefferson Alvarez Carles Hernandez-Ferrer Kenneth D. Mandl Sek Won Kong |
author_sort |
In-Hee Lee |
title |
WEScover: selection between clinical whole exome sequencing and gene panel testing |
title_short |
WEScover: selection between clinical whole exome sequencing and gene panel testing |
title_full |
WEScover: selection between clinical whole exome sequencing and gene panel testing |
title_fullStr |
WEScover: selection between clinical whole exome sequencing and gene panel testing |
title_full_unstemmed |
WEScover: selection between clinical whole exome sequencing and gene panel testing |
title_sort |
wescover: selection between clinical whole exome sequencing and gene panel testing |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2021-05-01 |
description |
Abstract Background Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted gene panel testing may be a dependable option to ascertain true negatives for genomic variants in known disease-associated genes. We developed a web-based tool to quickly gauge whether all genes of interest would be reliably covered by WES or whether targeted gene panel testing should be considered instead to minimize false negatives in candidate genes. Results WEScover is a novel web application that provides an intuitive user interface for discovering breadth and depth of coverage across population-scale WES datasets, searching either by phenotype, by targeted gene panel(s) or by gene(s). Moreover, the application shows metrics from the Genome Aggregation Database to provide gene-centric view on breadth of coverage. Conclusions WEScover allows users to efficiently query genes and phenotypes for the coverage of associated exons by WES and recommends use of panel tests for the genes with potential incomplete coverage by WES. |
topic |
Genetic testing False negative Coverage Whole exome sequencing Gene panel testing |
url |
https://doi.org/10.1186/s12859-021-04178-5 |
work_keys_str_mv |
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